Tools and services documentation 2
Version 17.1 by sarakonradi on 2021/04/27 15:14
Findable. Accessible. User-facing.
Welcome to the single entry point to user-level documentation for EBRAINS tools and services. Here, you can find a list of EBRAINS offerings, sorted by Service Category (SC), and their documentation links.
| fairgraph Python API for the Human Brain Project Neural Activity Resource, capable of changing, and working with Metadata | Arbor Arbor is a library for implementing performance portable network simulations of multi-compartment neuron models. | ||
| Bids Manager & Pipeline Bids Manager is a tool that allows various users to easily import and explore databases in BIDS format. Bids Pipeline, an extension of Bids Manager, allows to launch process on BIDS database. | BluePyMM Model Management Python Library | BluePyOpt BluePyOpt is an extensible framework for data-driven model parameter optimisation that wraps and standardizes several existing open-source tools. | |
| BrainScaleS | CoreNeuron CoreNeuron implements the core functionalities of the NEURON simulator targeting high efficiency when using millions of threads. | Elephant Elephant is an open-source Python library for the analysis of neurophysiology data, using Neo data structures. | |
| Fenix | HBP Validation Framework - Python Client A Python package for working with the Human Brain Project Model Validation Framework. | HiBoP 3D visualization software for intracranial EEG. | |
| Hodgkin Huxley Neuron Builder The Hodgkin-Huxley Neuron Builder web-application is a use case that allows the user to interactively go through the entire single cell model building pipeline. | Insite beta Insite provides live access to running neuronal simulations for in-transit visualization and analysis. | Interactive Atlas Viewer Interactive Atlas Viewer is a frontend module wrapping around nehuba.It provides additional features, such as metadata integration, data visualisation and a robust plugin system. | |
| JuGEx JuGEx links cytoarchitecture and gene expression to investigate multilevel human brain organization. | KnowledgeSpace Encyclopedia and open data access portal for neuroscience that serves as a framework where large-scale neuroscience projects can expose their data to the neuroscience community-at-large. | Multi-scale brain simulation with TVB-NEST Simulate multi-scale brain network models with TVB and NEST. | |
| NEST Desktop A web-based GUI application for NEST simulator. | NEST NEST is a simulator for spiking neural network models that focuses on the dynamics, size and structure of neural systems rather than on the exact morphology of individual neurons | NESTML A domain specific language to describe neuron models in NEST. | |
| NEURON Simulation enviroment for building and using computational models of neurons and networks of neurons | Neo an object model for handling electrophysiology data in multiple formats. | Neo Viewer Django/Angular software for graphing neural activity data (analog signals, spike trains etc.) read from Neo files. | |
| NeuroM NeuroM is a Python toolkit for the analysis and processing of neuron morphologies. | NeuroScheme NeuroScheme is a tool for navigating, exploring, creating and interacting with NeuroScience data using abstract, schematic or expressive representations. | NeuroTessMesh A Tool for the Generation and Visualization of Neuron Meshes and Adaptive On-the-Fly Refinement | |
| Neuromorphic Platform Python client Client software for the Human Brain Project Neuromorphic Computing Platform. | Neurorobotics Platform The NRP supports closed-loop neuroscience and embodied AI by connecting brains and bodies in simulation. | Nutil Nutil aims to both simplify and streamline the mechanism of pre-and-post processing 2D brain image data from mouse and rat. | |
| ODE-toolbox Automatic selection and generation of integration schemes for systems of ordinary differential equations. | PyJuGex JuGEx is an integrated framework of the AllenBrain and JuBrain atlases for statistical analysis of differential gene expression in the adult human brain. | PyNN A Python package for simulator-independent specification of neuronal network models. | |
| QuickNII QuickNII is a tool for user guided affine registration (anchoring) of 2D experimental image data, typically high resolution microscopic images, to 3D atlas reference space, facilitating data integration through standardized coordinate systems. | SLURM plugin for the co-allocation of compute and data resources A plugin for SLURM used for the co-allocation of compute and data resources. | SpiNNaker Jupyter Service | |
| SpiNNaker Local Boards | SpiNNaker Machine | SpiNNaker Remote Access | |
| SpiNNaker Software | SpiNNaker-NRP integration | TVB Brain Atlas Viewer An interactive viewer of human brain function. | |
| TVB image processing pipeline This pipeline combines the BIDS Apps mrtrix3_connectome, fmriprep and tvb_converter into a neuroimaging pipeline to compute structural and functional connectomes from MRI data. | TVB-HPC This is a Python package for generating code for parameter sweeps and Bayesian inversion. | The Virtual Brain "The Virtual Brain" Project (TVB Project) has the purpose of offering modern tools to the Neurosciences community, for computing, simulating and analyzing functional and structural data of human brains, brains modeled at the level of population of neurons. | |
| The Virtual Brain Web-App The Virtual Brain Web App at HBP. | Unicore A set of software components for federated access to high-performance compute and data resources. | ViSimpl ViSimpl integrates a set of visualization and interaction tools that provide a multi-view visual analysis of brain simultation data. | |
| VoluBA volumetric brain anchoring |
Support
In SGA3, the High Level Support Team (HLST, T4.13) is responsible for coordinating documentation efforts in EBRAINS. Contact the HLST if you have questions about this page or our tools, services and workflows.